https://github.com/nomad-coe/nomad-visu

https://github.com/nomad-coe/nomad-visu

Last synced: about 1 month ago
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• Host: GitHub
• URL: https://github.com/nomad-coe/nomad-visu
• Owner: nomad-coe
• Created: 2022-09-07T12:25:15.000Z (over 2 years ago)
• Default Branch: main
• Last Pushed: 2023-01-10T13:44:11.000Z (almost 2 years ago)
• Last Synced: 2024-04-24T11:54:50.817Z (8 months ago)
• Language: Python
• Homepage: https://nomad-coe.github.io/nomad-visu/
• Size: 9.07 MB
• Stars: 1
• Watchers: 3
• Forks: 0
• Open Issues: 1
• Metadata Files:
  • Readme: README.md

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README

        
# NOMAD-visu:

[![Tests](https://github.com/nomad-coe/nomad-visu/actions/workflows/python-package.yml/badge.svg)](https://github.com/nomad-coe/nomad-visu/actions/workflows/python-package.yml)

[![Docs](https://github.com/nomad-coe/nomad-visu/actions/workflows/python-mkdocs.yml/badge.svg)](https://nomad-coe.github.io/nomad-visu/)

A Python package for atomistic data visualisation

## Installation

You can install using `pip`:

```bash

pip install nomad-visu

```

## Quick start

Visualize octet binaries:

```python

import pandas as pd

from nomad_lab_visualizer import Visualizer

```

Load the data:

```python

df = pd.read_pickle('examples/octet_binaries/df')

regr_line_coefs = [0.11425013108281612, -1.48249992475763]

intercept = -0.1447151781886926

```

Define the features for the plots:

```python

features = ['((|IP_B  - EA_B |) / (r_p_A^2))', '((|r_s_A - r_p_B|) / exp(r_s_A))']

```

Finally display the visualizer:

```python

visualizer = Visualizer(

    df,

    features,

    features,

    target="Classification",

    #   path_to_structures='./octet_binaries/structures',

    regr_line_coefs=[regr_line_coefs, intercept],

    smart_fract=True,

    convex_hull=True,

)

visualizer.show()

```

## Development installation

Create a python environment for development:

```bash

mamba create -n nomad-visu-dev -c conda-forge python pip jupyter jupyterlab plotly ipywidgets py3dmol numpy scipy pandas scikit-learn setuptools pip-tools black mypy pytest flake8

mamba activate nomad-visu-dev

```

Install the python package in editable mode (i.e. setuptools "develop mode") from a local project path (`.`).

```bash

pip install -e ".[dev,test,docs]"

```

Run the python tests:

```bash

py.test

```